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- EMDB-60897: Cryo-EM structure of human XPR1 in complex with InsP6 in closed s... -

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Basic information

Entry
Database: EMDB / ID: EMD-60897
TitleCryo-EM structure of human XPR1 in complex with InsP6 in closed state - in the presence of KIDINS220-1-432 without substrate KH2PO4
Map data
Sample
  • Complex: XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: CHOLESTEROL
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: PALMITIC ACID
  • Ligand: ARACHIDONIC ACID
KeywordsSLC53A1 / transporter / phosphate / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / phosphate ion transmembrane transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / efflux transmembrane transporter activity / response to virus / virus receptor activity / plasma membrane
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZuo P / Liang L / Yin Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate.
Authors: Peng Zuo / Weize Wang / Zonglin Dai / Jiye Zheng / Shang Yu / Guangxi Wang / Yue Yin / Ling Liang / Yuxin Yin /
Abstract: Inorganic phosphate (Pi) is essential for life, and its intracellular levels must be tightly regulated to avoid toxicity. XPR1, the sole known phosphate exporter, is critical for maintaining this ...Inorganic phosphate (Pi) is essential for life, and its intracellular levels must be tightly regulated to avoid toxicity. XPR1, the sole known phosphate exporter, is critical for maintaining this balance. Here we report cryo-EM structures of the human XPR1-KIDINS220 complex in substrate-free closed and substrate-bound outward-open states, as well as an XPR1 mutant in a substrate-bound inward-facing state. In the presence of inositol hexaphosphate (InsP) and phosphate, the complex adopts an outward-open conformation, with InsP binding the SPX domain and juxtamembrane regions, indicating active phosphate export. Without phosphate or InsP, the complex closes, with transmembrane helix 9 blocking the outward cavity and a C-terminal loop obstructing the intracellular cavity. XPR1 alone remains closed even with phosphate and InsP. Functional mutagenesis shows that InsP, whose levels vary with Pi availability, works with KIDINS220 to regulate XPR1 activity. These insights into phosphate regulation may aid in developing therapies for ovarian cancer.
History
DepositionJul 20, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60897.png

Downloads & links

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Map

FileDownload / File: emd_60897.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.47230074 - 0.66314775
Average (Standard dev.)-0.0002289887 (±0.011395712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60897_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60897_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4

EntireName: XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4
Components
  • Complex: XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: CHOLESTEROL
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: PALMITIC ACID
  • Ligand: ARACHIDONIC ACID

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Supramolecule #1: XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4

SupramoleculeName: XPR1-KIDINS220-1-432 in complex with InsP6 without substrate KH2PO4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 53 member 1

MacromoleculeName: Solute carrier family 53 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.673992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQN ELQSSLDAQK ESTGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI L KKHDKILE ...String:
MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQN ELQSSLDAQK ESTGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI L KKHDKILE TSRGADWRVA HVEVAPFYTC KKINQLISET EAVVTNELED GDRQKAMKRL RVPPLGAAQP APAWTTFRVG LF CGIFIVL NITLVLAAVF KLETDRSIWP LIRIYRGGFL LIEFLFLLGI NTYGWRQAGV NHVLIFELNP RSNLSHQHLF EIA GFLGIL WCLSLLACFF APISVIPTYV YPLALYGFMV FFLINPTKTF YYKSRFWLLK LLFRVFTAPF HKVGFADFWL ADQL NSLSV ILMDLEYMIC FYSLELKWDE SKGLLPNNSE ESGICHKYTY GVRAIVQCIP AWLRFIQCLR RYRDTKRAFP HLVNA GKYS TTFFMVTFAA LYSTHKERGH SDTMVFFYLW IVFYIISSCY TLIWDLKMDW GLFDKNAGEN TFLREEIVYP QKAYYY CAI IEDVILRFAW TIQISITSTT LLPHSGDIIA TVFAPLEVFR RFVWNFFRLE NEHLNNCGEF RAVRDISVAP LNADDQT LL EQMMDQDDGV RNRQKNRSWK YNQSISLRRP RLASQSKARD TKVLIEDTDD EANTSRENLY FQ

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 6 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #6: ARACHIDONIC ACID

MacromoleculeName: ARACHIDONIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: ACD
Molecular weightTheoretical: 304.467 Da
Chemical component information

ChemComp-ACD:
ARACHIDONIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88082
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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